I am able to read out the Flash ID and CFI table now with the modified GB cart flasher!
I am using a MX29LV640 in 8bit mode (since native 8 bit flashes are hard to find or too expansive nowadays). It turns out that though 8bit mode is enabled (means an additional A0 bit), the device is still expecting the address for things like CFI appears on the original 16bit mode address bus which is A[x:1] instead of A[x:0] for the 8bit mode address bus. And I also had some soldering issue, took me several days to debug and find out what it going on. But now it is working! (As you can see, 51 52 59 represents "QRY" which is the start of the CFI table, and other things well match the datasheet)